[gmx-users] New residue in FF does not bond to others.

[Dawid das]

These are lines that cause trouble:

ERROR 1 [file mCherry7.top, line 18183]:
  No default U-B types


ERROR 2 [file mCherry7.top, line 18250]:
  No default U-B types


ERROR 3 [file mCherry7.top, line 25379]:
  No default Proper Dih. types


ERROR 4 [file mCherry7.top, line 25380]:
  No default Proper Dih. types


ERROR 5 [file mCherry7.top, line 25383]:
  No default Proper Dih. types


ERROR 6 [file mCherry7.top, line 25386]:
  No default Proper Dih. types


ERROR 7 [file mCherry7.top, line 25387]:
  No default Proper Dih. types


ERROR 8 [file mCherry7.top, line 25388]:
  No default Proper Dih. types


ERROR 9 [file mCherry7.top, line 25455]:
  No default Proper Dih. types


ERROR 10 [file mCherry7.top, line 25457]:
  No default Proper Dih. types

ERROR 11 [file mCherry7.top, line 25458]:
  No default Proper Dih. types

 Now in these files which I have already uploaded I have only added two
extra lines just above [ angles ] section of CH6 residue in aminoacids.rtp
(lines 1793 and 1794):
        MC3     +N      0.1345  154808.0
        MN1     -C      0.139   173594.2

I have not changed anything else in any other file.
Now the problem is that I have consecutive residues Phe65-CH6-Ser69. MN1
atom of CH6 is supposed to be bonded to C atom of Phe65. MC3 atom of CH6 is
supposed to be bonded to atom NH1 of Ser69. C atom of Phe65 is not supposed
to be bonded to NH1 atom of Ser69 but it is in my *top file. What other
files do you need?

Best wishes,

Dawid Grabarek




2014-08-06 20:04 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 8/6/14, 12:52 PM, Dawid das wrote:
>
>> Yes CH6 is defined as a Protein. In fact pdb2gmx sees two chains. How to
>> work it out then?
>>
>>
> You'll need to provide files and describe exactly what the problems are
> (lines in the topology, please) and what changes you have made since the
> last bundle of files you uploaded.
>
> -Justin
>
>
>
>> 2014-08-06 19:45 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>>>
>>> On 8/6/14, 12:04 PM, Dawid das wrote:
>>>
>>>  Cause now what happens is that grompp requires bonding parameters for
>>>> atoms
>>>> which are actually bonded and for which are not (angle and dihedral
>>>> parameters), e.g. CH6-Ser69 and CH6-Phe65 is what I want but I do not
>>>> want
>>>> connection between Ser69-Phe65. Now grompp asks me about bonding
>>>> paramters
>>>> for atoms which build all three residues while these residues are
>>>> separated
>>>> by more than 4 atoms.
>>>>
>>>>
>>>>  Properly constructed .rtp entries will not need manual editing, which
>>> is
>>> very error-prone.  You're using lots of strange atom names, so you need
>>> to
>>> establish proper bonding from the CH6 residue; the +/- mechanism in
>>> flanking residues will fail.  If you're getting connections between
>>> non-consecutive residues, that suggests a break in the chain when being
>>> processed by pdb2gmx; make sure CH6 is defined as a Protein residue in
>>> residuetypes.dat.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>